# Top level Makefile for HMMER3
# 
# On most systems, to build H3 you should only need:
#     % ./configure; make
#
# Optionally, you can run a test suite:
#     % make check
#
# And optionally, you can install everything more permanently:
#     % make install
#
# For more information, see the Installation chapter of the HMMER
# User's Guide.
#


# VPATH and shell configuration
#
top_srcdir     = @top_srcdir@
srcdir         = @srcdir@
VPATH          = @srcdir@
SHELL          = /bin/sh

# location of easel
ESLDIR         = @HMMER_ESLDIR@

# location of libdivsufsort for suffix array creation
SADIR          = @HMMER_SADIR@


# Package information
#
PACKAGE         = @PACKAGE_NAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PACKAGE_TARNAME = @PACKAGE_TARNAME@

# Installation targets
#
prefix      = @prefix@
exec_prefix = @exec_prefix@
datarootdir = @datarootdir@
bindir      = @bindir@
libdir      = @libdir@
includedir  = @includedir@
mandir      = @mandir@
docdir      = @docdir@
pdfdir      = @pdfdir@
mandir      = @mandir@
man1dir     = ${mandir}/man1
man1ext     = .1

# Compiler configuration
#
CC        = @CC@
CFLAGS    = @CFLAGS@ @PTHREAD_CFLAGS@ @PIC_FLAGS@
LDFLAGS   = -static @LDFLAGS@
SIMDFLAGS = @SIMD_CFLAGS@
CPPFLAGS  = @CPPFLAGS@

# Other tools
#
AR        = @AR@ 
RANLIB    = @RANLIB@
INSTALL   = @INSTALL@

# beautification magic stolen from git 
#
QUIET_SUBDIR0 = +${MAKE} -C #space separator after -c
QUIET_SUBDIR1 = 
ifndef V
	QUIET_CC      = @echo '    ' CC $@;
	QUIET_GEN     = @echo '    ' GEN $@;
	QUIET_AR      = @echo '    ' AR $@;
	QUIET_SUBDIR0 = +@subdir=
	QUIET_SUBDIR1 = ; echo '    ' SUBDIR $$subdir; \
		        ${MAKE} -C $$subdir
endif

# Programs installed by HMMER (stable, documented)
#
PROGS = alimask\
	hmmalign\
	hmmbuild\
	hmmconvert\
	hmmemit\
	hmmfetch\
	hmmpress\
	hmmscan\
	hmmsearch\
	hmmsim\
	hmmstat\
	jackhmmer\
	phmmer\
	nhmmer\
	nhmmscan\
	hmmpgmd

.PHONY: all dev check pdf install uninstall clean distclean TAGS

# all: Compile all documented executables.
#      (Excludes test programs.)
#
all: 
	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} all
	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} all
	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} all
	${QUIET_SUBDIR0}profmark      ${QUIET_SUBDIR1} all

# dev: compile all executables, including drivers.
#
dev: 
	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} dev
	${QUIET_SUBDIR0}${SADIR}   ${QUIET_SUBDIR1} all
	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} dev
	${QUIET_SUBDIR0}profmark   ${QUIET_SUBDIR1} dev

# tests: compile all test drivers for 'make check'
#
tests:
	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} tests
	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} tests

# check: Run test suites.
#
check:
	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} tests
	${QUIET_SUBDIR0}${SADIR}   ${QUIET_SUBDIR1} all	
	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} tests
	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} check
	${QUIET_SUBDIR0}testsuite  ${QUIET_SUBDIR1} check

# pdf: compile the User Guides.
#
pdf:
	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf

# install: installs the binaries in ${bindir}/
#          When man pages are done, will install man pages in MANDIR/man1/  (e.g. if MANSUFFIX is 1)
#          Creates these directories if they don't exist.
#          Prefix those paths with ${DESTDIR} (rarely used, usually null;
#          may be set on a make command line when building contrib RPMs).
install: 
	${INSTALL} -d ${DESTDIR}${bindir}
	${INSTALL} -d ${DESTDIR}${libdir}
	${INSTALL} -d ${DESTDIR}${includedir}
	${INSTALL} -d ${DESTDIR}${man1dir}
	${INSTALL} -d ${DESTDIR}${pdfdir}
	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} install
	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} install

# uninstall: Reverses the steps of "make install".
#
uninstall: 
	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} uninstall
	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} uninstall

# "make clean" removes almost everything except configuration files.
#
clean:
	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} clean
	${QUIET_SUBDIR0}profmark      ${QUIET_SUBDIR1} clean
	${QUIET_SUBDIR0}testsuite     ${QUIET_SUBDIR1} clean
	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean
	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} clean
	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} clean
	-rm -f *.o *~ Makefile.bak core TAGS gmon.out

# "make distclean" leaves a pristine source distribution.
#
distclean:
	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} distclean
	${QUIET_SUBDIR0}profmark      ${QUIET_SUBDIR1} distclean
	${QUIET_SUBDIR0}testsuite     ${QUIET_SUBDIR1} distclean
	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean
	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} distclean
	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} distclean
	-rm config.log config.status
	-rm -rf autom4te.cache
	-rm -f *.o *~ Makefile.bak core TAGS gmon.out
	-rm -f cscope.po.out cscope.out cscope.in.out cscope.files
	-rm -f src/impl
	-rm Makefile
#Use 'ifneq' instead of 'test -e' because the '+@' in QUIET_SUBDIR0 can't
#be passed to the shell. Note that ifneq breaks if indented.
ifneq (,$(wildcard ./release-notes/LICENSE.sh))
	-rm -f release-notes/LICENSE.sh
endif


TAGS:
	./makeTAGS.sh



################################################################
# HMMER - Biological sequence analysis with profile HMMs
# Version 3.1b3; July 2016
# Copyright (C) 2016 Howard Hughes Medical Institute.
# Other copyrights also apply. See the COPYRIGHT file for a full list.
# 
# HMMER is distributed under the terms of the GNU General Public License
# (GPLv3). See the LICENSE file for details.
################################################################
